Molecular Dynamics - Simulation Analysis and Preparation Suite
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Updated
Sep 4, 2024 - Python
Molecular Dynamics - Simulation Analysis and Preparation Suite
A project (and object) for storing, manipulating, and converting molecular mechanics data.
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
This code adds custom-made amino acids to the GROMACS forcefield directory.
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
This repo contains a python script to obtain solvent sites according to https://watclust.wordpress.com/methodology/ using as input molecular dynamics in AMBER format (https://ambermd.org/).
A Package for Parametrization of Molecular Mechanics Force Fields
Python-based softwares for QM and MD data extraction.
A command line application to launch molecular dynamics simulations with OpenMM
A Snakemake workflow for analyzing AMBER molecular dynamics simulations.
[early prototype testing] An interactive point-and-click text interpreter with logic in python and UI in your browser.
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.
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